So I finally got around to fixing all of the issues noted in the post above from 19 September 2016.
The tank paint had bubbled up due to a pin-hole leak in the area where the Honda emblem had been. I ground-down to the bare metal and used another coat of Caswell on the inside and dabbed a bunch in that area of the outside as well.
In taking the rear fender off I discovered I had too little clearance between it and the tire at very front edge. This resulted in "tire dust" and yellowed, burnt clear coat.
I sanded all of the the chainguard and fender and tank with 600 wet. Then I masked off areas where I was hoped to only have to spray clear and sanded the damaged areas with 80 to give the filler something to bite to. I filled and sanded the damaged areas.
I decided it was easier to completely repaint the rear fender which meant remasking the scallop design and shooting silver over the charcoal metallic. In the end I re-shot KD3000 primer/sealer plus gray and/or silver over 80% of the tank, 1/2 of the chainguard and all of the fender. All of the parts got three new coats of House of Kolor clear.
During reassembly I cut and re-welded the front fender bracket to pull the front of the fender nearly 1/2-inch further away from the tire and I stiffened up the shocks a couple of clicks.
It was certainly annoying to have to redo these parts, there is nothing quite like learning the hard way from ones mistakes, eh? So now she is back together and better than ever.